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Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

McGaughran, Angela

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Background: Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wetlab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample...[Show more]

dc.contributor.authorMcGaughran, Angela
dc.date.accessioned2020-09-24T03:08:39Z
dc.date.available2020-09-24T03:08:39Z
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/1885/211558
dc.description.abstractBackground: Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wetlab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years. Results: I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing. Conclusions: Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.
dc.description.sponsorshipThis research was funded by the Australian Research Council (Discovery Early Career Researcher Award DE160100685)
dc.format.mimetypeapplication/pdf
dc.language.isoen_AU
dc.publisherBioMed Central
dc.rights© The Author(s).
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceBMC Genomics
dc.titleEffects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume21
dc.date.issued2020
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.absfor060408 - Genomics
local.identifier.ariespublicationa383154xPUB10732
local.publisher.urlhttp://www.biomedcentral.com/bmcgenomics/
local.type.statusPublished Version
local.contributor.affiliationMcGaughran, Angela, College of Science, ANU
dc.relationhttp://purl.org/au-research/grants/arc/DE160100685
local.bibliographicCitation.issue1
local.bibliographicCitation.startpage1
local.bibliographicCitation.lastpage10
local.identifier.doi10.1186/s12864-020-6594-0
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2020-06-28T08:16:22Z
dcterms.accessRightsOpen Access
dc.provenance© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
dc.rights.licenseCreative Commons Attribution 4.0 International License
CollectionsANU Research Publications

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